Dataset Information

Transcriptome analysis during ripening of table grape berry cv. Thompson Seedless.

ABSTRACT: Ripening is one of the key processes associated with the development of major organoleptic characteristics of the fruit. This process has been extensively characterized in climacteric fruit, in contrast with non-climacteric fruit such as grape, where the process is less understood. With the aim of studying changes in gene expression during ripening of non-climacteric fruit, an Illumina based RNA-Seq transcriptome analysis was performed on four developmental stages, between veraison and harvest, on table grapes berries cv Thompson Seedless. Functional analysis showed a transcriptional increase in genes related with degradation processes of chlorophyll, lipids, macromolecules recycling and nucleosomes organization; accompanied by a decrease in genes related with chloroplasts integrity and amino acid synthesis pathways. It was possible to identify several processes described during leaf senescence, particularly close to harvest. Before this point, the results suggest a high transcriptional activity associated with the regulation of gene expression, cytoskeletal organization and cell wall metabolism, which can be related to growth of berries and firmness loss characteristic to this stage of development. This high metabolic activity could be associated with an increase in the transcription of genes related with glycolysis and respiration, unexpected for a non-climacteric fruit ripening.

SUBMITTER: Balic I

PROVIDER: S-EPMC5761854 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Transcriptome analysis during ripening of table grape berry cv. Thompson Seedless.

Balic Iván I Vizoso Paula P Nilo-Poyanco Ricardo R Sanhueza Dayan D Olmedo Patricio P Sepúlveda Pablo P Arriagada Cesar C Defilippi Bruno G BG Meneses Claudio C Campos-Vargas Reinaldo R

PloS one 20180110 1

Ripening is one of the key processes associated with the development of major organoleptic characteristics of the fruit. This process has been extensively characterized in climacteric fruit, in contrast with non-climacteric fruit such as grape, where the process is less understood. With the aim of studying changes in gene expression during ripening of non-climacteric fruit, an Illumina based RNA-Seq transcriptome analysis was performed on four developmental stages, between veraison and harvest, ...[more]

PMID: 29320527

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Project description:BackgroundEarly ripening is an important desirable attribute for fruit crops. 'Kyoho' is a popular table grape cultivar in many Asian countries. 'Fengzao' is a bud mutant of 'Kyoho' and ripens nearly 30 days earlier than 'Kyoho'. To identify genes controlling early fruit development and ripening in 'Fengzao', RNA-Seq profiles of the two cultivars were compared at 8 different berry developmental stages in both berry peel and flesh tissues.MethodsRNA-Seq profiling of berry development between 'Kyoho' and 'Fenzhao' were obtained using the Illumina HiSeq system and analyzed using various statistical methods. Expression patterns of several selected genes were validated using qRT-PCR.ResultsAbout 447 millions of RNA-Seq sequences were generated from 40 RNA libraries covering various different berry developmental stages of 'Fengzao' and 'Kyoho'. These sequences were mapped to 23,178 and 22,982 genes in the flesh and peel tissues, respectively. While most genes in 'Fengzao' and 'Kyoho' shared similar expression patterns over different berry developmental stages, there were many genes whose expression were detected only in 'Fengzao' or 'Kyoho'. We observed 10 genes in flesh tissue and 22 genes in peel tissue were differentially expressed at FDR ≤ 0.05 when the mean expression of 'Fengzao' and 'Kyoho' were compared. The most noticeable one was VIT_214s0030g00950 (a superoxide dismutase gene). This ROS related gene showed lower expression levels in 'Fengzao' than 'Kyoho' in both peel and flesh tissues across various berry developmental stages with the only exception at véraison. VIT_200s0238g00060 (TMV resistance protein n-like) and VIT_213s0067g01100 (disease resistance protein at3g14460-like) were the two other noticeable genes which were found differentially expressed between the two cultivars in both peel and flesh tissues. GO functional category and KEGG enrichment analysis of DEGs indicated that gene activities related to stress and ROS were altered between the two cultivars in both flesh and peel tissues. Several differentially expressed genes of interest were successfully validated using qRT-PCR.ConclusionsComparative profiling analysis revealed a few dozens of genes which were differentially expressed in the developing berries of 'Kyoho' and its early ripening mutant 'Fengzao'. Further analysis of these differentially expressed genes suggested that gene activities related to ROS and pathogenesis were likely involved in contributing to the early ripening in 'Fengzao'.

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Dataset Information

Transcriptome analysis during ripening of table grape berry cv. Thompson Seedless.

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Transcriptome analysis during ripening of table grape berry cv. Thompson Seedless.

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